A pox on your numbered references, redux

April 2, 2013


I am preparing a manuscript for PLOS ONE, which uses numbered references rather than author+date citations like sane journals. And I am hating it. I am taking perfectly good statements like:

Juvenile sauropods have proportionally short cervicals (Wedel et al. 200: 368–369, Fig. 14, and Table 4)

And reformatting them as:

Juvenile sauropods have proportionally short cervicals [31]: 368–369, Fig. 14, and Table 4.

Which doesn’t look right at all.

My question: how, when using numbered references, can I properly refer to page-range and figure number? Because there has to be a way — doesn’t there?

Surely it can’t be the case that in the culture of numbered-reference journals, you just don’t bother to specify with any more precision than pointing at a 46-page paper? I know Science ‘n’ Nature don’t care much about science or nature, but they can’t be that sloppy, can they? And if they are, I’d be horrified to find that the PLOS journals are so infected with me-too that they’re prepared to copy such poor practice?

33 Responses to “A pox on your numbered references, redux”

  1. I’ve hit a similar glitch with wikipedia. There, the solution is cumbersome to create but simple: you have two sets of references, the first with letters ([A], [B],…), which cites the page or pages or figure in a reference that is numbered ([1], [37], etc.). You end up having two lists…..


    and I am currently writing a PLOS ONE manuscript (for a collection, thus I must submit there), and I have the same stupid problem. Maybe Andy Farke can enlighten us?

  2. Mike Taylor Says:

    I think you and I are writing for the same collection :-)

    On 2 April 2013 22:58, Sauropod Vertebra Picture of the Week

  3. I think you think exactly what I think. ;)

  4. Mike Taylor Says:

    In that case, you’re late submitting!

    On 2 April 2013 23:05, Sauropod Vertebra Picture of the Week

  5. April 30! But then it has to be perfect, which it will not be….. ugh!

  6. Mike Taylor Says:

    Dude, I have bad news for you. Check your email from 30th January: “Now for the details, deadlines first. We […] still would like to stick with the March 31st deadline in order to launch the collection in time.”

  7. Dude, I have good news for me: I just re-checked my email from March 22, which specifically said March 15 for language checks, April 30 with PLOS ONE.

  8. Andy Farke Says:

    Speaking as Private Citizen Farke (i.e., not citing Official PLOS Policy, but simply what I recommend to authors when acting as academic editor), I would go with:

    Juvenile sauropods have proportionally short cervicals ([31]: 368–369, fig. 14, table 4).

    I usually lower-case the “fig.” and “table”, to contrast with the upper-case “Figure X” or “Table X” that refer to figures and tables in the manuscript itself. The idea here is to prevent the minions in the production office from accidentally linking to an internal figure/table (which has happened before–downside of no author proofs).

  9. Andy, no author proofs?

    This has me seriously considering NOT to submit to PLOS ONE ever.

  10. and many thanks for your answer re citing figs and pages! :)

  11. Mike Taylor Says:

    Thanks for this, Andy. So essentially what I did, but with the whole citation wrapped in parentheses. I’ll modify my citations accordingly.

    I do agree that the upper/lower-case conventions for citing figures and tables that are from this/other manuscripts is a useful one.

    Lack of author proofs is pretty terrifying given the huge number of mistakes that I nearly always spot in proof PDFs, and especially given the fair proportion that were usually introduced by the journal. But it’s a well-known PLOS ONE corner-cut, and it’s a bit late to complain about it now, Heinrich :-) I see this not necessarily as a downside, but as a reason to have PLOS accept camera-ready copy that needs no further messing by editorial staff.

  12. Mike,
    a) I never knew &
    b) could never imagine
    that a journal does not give an author the chance to check that his work is portrayed correctly!

    That said, I am NOT afraid of someone mis-fixing my mistakes. But I have, in the past, seen editorial teams fuck up perfectly fine papers, “correcting” obvious mistakes – even when supposedly they wouldn’t do it (as PLOS says they don’t).

  13. Bill Says:

    What’s wrong with this? —

    Juvenile sauropods have proportionally short cervicals [31, Fig. 14 & Table 4].

    You don’t need page numbers AND figure/table references, and you only need those for enormous (usually reference) papers.

  14. Bill Says:

    Wait, Private Citizen Farke is right — lowercase F and T.

  15. Mike Taylor Says:

    I think [31, fig. 14 & table 4] is OK, but Zotero won’t render it that way.

    And you do, at least sometimes, need both page numbers and figure/table references, for cases (like the one I used in the example) where something is both discussed in the text and illustrated.

  16. yeah, you need to edit the zotero style for PLOS ONE for this.

    however, if you add the pages and figures as a suffix to the zotero entry, things should work ;)

  17. Mike Taylor Says:

    yeah, you need to edit the zotero style for PLOS ONE for this.

    Someone certainly should. But it won’t be me — I am a total Zotero n00b.

    however, if you add the pages and figures as a suffix to the zotero entry, things should work ;)

    They should; but they don’t :-)

  18. [1, fig. 4 & p. 31-34] is what I get when I use “, fig. 4 & p. 31-34” as a suffix

  19. so either do it Andy’s way, with the zotero field containing only the [ ] with the number, or use a suffix and have the pages and tables listed within the [ ]

  20. For what it’s worth, LaTeX will give you something like [31, extra info for locating specifics] when using BiBTeX. So my vote goes to Bill’s version.

    Or even [Wedel et al. 2000, extra info] if that floats your boat.

    So I would write something like

    [31, pp 368–369, fig. 14 & table 4]

    PS I hope you aren’t going to refer to Wedel et al. 200, because your field is fond of citing old references, but not that old.

  21. […] I am preparing this paper from PLOS ONE, with its stupid numbered-references system, I am finally getting to grips with a reference-management system. Specifically, Zotero, which is […]

  22. Nico (@nfanget) Says:

    Should you wish to write for Nature, we do allow citing parts of books, the reference(s) would look something like
    4. Smith, J. A Very Interesting Book (ed. Blogg, W.) 45-67 (Big Publisher, 2002).
    5. Smith, J. A Very Interesting Book (ed. Blogg, W.) 2-12 (Big Publisher, 2002).
    ans so on.

    The restriction is more imposed by our ref limits, but that’s an entire other debate.

    To reference specific figures etc I like this format:
    see Fig. 1 and Table 8 in ref. 4

    which Zotero can do, IIRC.

  23. Mike Taylor Says:

    Thanks, Nico. I doubt that I will ever write for Nature (it would be hypocritical) but it’s good to see how other journals handle this. Having separate references for citing different parts of the same work seems very inefficient.

  24. Nico (@nfanget) Says:

    Well, I didn’t really expect to see your name in an author list in our back half ;-)

    We can be quite flexible with our style when required though (I am the official Keeper of the Style Guide here), so if it was important to save on refs we could probably use something like “see pages 34-38 in ref. 4”. Letters/Articles usually do not cite that many books/book parts, and Reviews have enough pages to allow for duplicate citations, so the problem just hasn’t arisen, AFAIK.

  25. Nico (@nfanget) Says:

    Oh and in defence of numbered refs (I am quite fond of them), here is an extract of “Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus”, published yesterday:

    “the V1/V2 region, glycan-associated C3/V3 on gp120, and the CD4-binding site1, 2, 3, 4, 5, 6, 7, 8, 9.”

    That would look messy with author-date format. Horses for courses.

  26. well, not that messy – the call-out is not in the middle of the sentence.

    Honestly, that#s the one thing numbered refs have going for them.

  27. […] at SV-POW!, we are an equal-opportunity criticiser of publishers: Springer, PLOS, Elsevier, the Royal Society, Nature, we don’t care. We call problems as we see them, where […]

  28. David Marjanović Says:

    In case anyone’s still reading this: I’ve published in PLOS ONE and…

    1) I’ve tried the “[31: fig. 14, table 4]” format and was told in no uncertain terms that that’s not acceptable: only the reference number may be in brackets. “([31]: fig. 14, table 4)” it was, then. Can end up clunky sometimes.

    2) Although PLOS journals don’t produce page proofs, accepted manuscripts are not published there as-is. There is a copyediting process, and the people doing it are unfamiliar with some pretty basic conventions. In my paper, I often put a question mark at the beginning of a word, as in “the Miocene ?Ichthyosaura randeckensis“. Every single time, even in the abstract, the copyeditors moved the question mark to the end of the preceding word, as in “the Miocene? Ichthyosaura randeckensis“. I had no way to find out before the paper was published. Let me stress once more that neither my coauthor nor I at all doubt the Miocene age of the species; its assignment to Ichthyosaura is what is questionable (as the paper explains in detail).

  29. Mike Taylor Says:

    David, that is terrible. Do not accept it: get straight back to your handling editor, explain what has happened and demand a correction. If he or she doesn’t help, go over their head.

  30. PLOS sucks in this respect, as should be well known.

  31. Mike Taylor Says:

    Not offering proofs is bad. (PeerJ offers them, as part of their lower-cost service.) But, OK, that’s how it goes.

    Unilaterally changing the meaning of an author’s paper and not letting them see it until it’s published is a hundred times worse. It would be flatly unacceptable from any publisher, let alone one of the good guys.

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